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| analysis.averageCorrelation | Predefined enrichment analyses |
| analysis.averageTStatistic | Predefined enrichment analyses |
| analysis.customOverrepresentation | Predefined enrichment analyses |
| analysis.globalAncova | Predefined enrichment analyses |
| analysis.globalTest | Predefined enrichment analyses |
| analysis.gsea | Predefined enrichment analyses |
| analysis.overrepresentation | Predefined enrichment analyses |
| createSummaryTable | Create an overview table for an analysis |
| evaluateGeneSetUncertainty | Quantify gene set uncertainty |
| filterGeneSets | Filtering of gene sets |
| geneSetAnalysis | Main interface for enrichment analyses. |
| GiANT | Enrichment analysis |
| global | Global analyses |
| global.ancova | Global analyses |
| global.overrepresentation | Global analyses |
| global.test | Global analyses |
| gls | Gene-level statistics |
| gls.cor | Gene-level statistics |
| gls.foldChange | Gene-level statistics |
| gls.moderateTStatistic | Gene-level statistics |
| gls.nBinomTest | Gene-level statistics |
| gls.regression | Gene-level statistics |
| gls.tStatistic | Gene-level statistics |
| gsAnalysis | Gene set analysis. |
| gss | Gene set statistics |
| gss.enrichmentScore | Gene set statistics |
| gss.fisherExactTest | Gene set statistics |
| gss.gsz | Gene set statistics |
| gss.maxmean | Gene set statistics |
| gss.mean | Gene set statistics |
| gss.median | Gene set statistics |
| gss.sum | Gene set statistics |
| gss.wilcoxonRankTest | Gene set statistics |
| hist.gsaResult | Null distribution histogram and statistic of the input set for enrichment analyses. |
| mergeProbesForGenes | Merge multiple probes for one gene |
| parseGmt | Venn Euler Diagramm |
| plot.uncertaintyResult | Plots the results of an uncertainty analysis. |
| plotOverrepresentation | Plot overlap of gene sets and core set |
| predefinedAnalyses | Predefined enrichment analyses |
| preprocessGeneSets | Eliminate unknown genes from gene sets |
| preprocessGs | Eliminate unknown genes from gene sets |
| significance | Significance assessment |
| significance.permutation | Significance assessment |
| significance.restandardization | Significance assessment |
| significance.sampling | Significance assessment |
| summary.gsaResult | Summarize gene set analysis results |
| transformation | Transformations |
| transformation.abs | Transformations |
| transformation.adjust | Transformations |
| transformation.adjustAndBinarize | Transformations |
| transformation.binarize | Transformations |
| transformation.localFdr | Transformations |
| transformation.rank | Transformations |
| transformation.square | Transformations |